You will typically want more clearance on the exhaust valve due to heat expansion.
General rule of thumb is .080" for the intake valve and .100" for the exhaust valve.
As the powerband goes up, the clearance needs to be increased.
Lift has very little to do with piston to valve clearance.
I would look into individual valve timing events (IO, IC, EO, EC) and the amount of time the valves are open (duration).
Early intake opening and late exhaust valve closings are a big contributer to piston to valve contact. This is known as the period of overlap, when both valves are open at the same time.
It is not based off peak gross lift.
Now, I would be careful on getting a thicker headgasket, because that will hurt the quench area a bit.
With your heads being shaved .040", you need to check piston to valve clearance yourself

It just makes it that much more crucial.